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You can add your different queries in the jdbc xml as individual beans and then use record adapters in the pipeline to invoke it. The query/bean id has to be mapped in the pass through tab(if i remember correctly).
If you open Developer Studio, go to Help > Developer Studio Contents.
Under the Contents Tab on the left side, if you go to:
Preparing Data, Properties and Dimensions > Preparing your source data > Importing Your Source Data > Input Formats, you'll see a heading for JDBC.
This is the quickest/simplest way to do it. There's also more advanced functionality available (through Spring, an AdvancedJDBCColumnHandler, etc.) but this should at least get you started...